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The Matrix was one of the top grossing, and most talked about movies of the past decade. It revolutionized the technology of making movies, and created a huge base of fans who waited for the completion of the trilogy. The problem, though, was that the trilogy ended, and many of the fans just didn’t get it. The complex story ended in what looked like a truce, instead of a win for humanity. What’s more, it seemed confusing and pointless.
I’ve watched all three movies many, MANY times. I’ll play the trilogy while I work on the computer, or do other things. I’m not a Matrix fanatic, mind you. It’s just a good movie to have on in the background.
As a result, I’ve been able to understand the story much better. I’ve dissected some key parts of the dialogue, and come to understand more about the motivations of various characters. In an effort to help you understand, I’ll pass along what I’ve learned.

Let’s start with the setup. In the Animatrix shorts, we learn about the history of the Matrix. Mankind created robots as helpers, and kept them under absolute control. In a key moment of political upheaval, war began between man and machines. The machines were exiled to the Middle East desert, where they grew and prospered. Eventually, the war between man and the machines continued, and the machines won. In the process, mankind “scorched the sky” to prevent the machines receiving solar power.
This led the machines to enslave mankind, to use them as batteries and provide power. This process was made easier by the creation of the Matrix, a false world in which the minds of mankind interacted with the world through programs. The machines also interacted with the Matrix through programs, in order to control mankind easier.
You knew all that. That’s the easy stuff.
Enter two main characters; The Architect and The Oracle.
The Architect is a program whose job is to create The Matrix. He looks at problems and makes changes to head them off. When mankind causes problems within the matrix, he improves the system to gain more control over them. Perfection is his goal.
The Oracle is a program whose job is to bring perfection to the Matrix by analyzing mankind. She looks at how the human mind works, and how this information can be used to improve the system and gain more control over mankind. Perfection is her goal.
Machinekind demands absolute control over humanity. Allowing humanity to thrive in their absence has, to this point, resulted in destruction and imperfection.
Enter “The One.” What the Architect said to Neo was true. We are looking at the fifth version of the Matrix. A small group of humans was allowed to exit the Matrix. They caused problems, which exposed weaknesses of the Matrix. Eventually, one of them emerged who had greater access to the machine language of the Matrix, and thus greater power. Inside this “One” was program code which exposed the weaknesses of the machines. When this “One” emerged, he eventually worked his way to The Architect. The code was extracted from him. At this point, Zion would be destroyed, “The One” would select a group of humans to remove from the Matrix, and the Matrix would be completely remade using this new knowledge, making it more perfect. The select group of humans would then become the new Zion, and the system would begin again. At all times, it is the machines who are in control.
The Architect states that humans accept the Matrix very well, as long as they are given a choice. This choice need only be made at a subconscious level. Those who choose to be a part of the Matrix live unquestioningly within the construct, and have no problems. Those who choose, unconsciously, to not be a part of the Matrix, never quite feel right. If they are lucky, they will be given the option of escaping the Matrix, as Neo was.
This time around, though, The Oracle sees something different. Her entire job is to study the humans. What she sees changes everything. This is the key point of the movie. The Oracle knows that the key to perfection in the Matrix is to stop trying to control those who decide to deny the programming. This is contrary to everything that the Machines believe. The machines demand absolute control. She knows that perfection can be gained only by giving up control over those who choose to be uncontrollable.
This means that there are two wars. The first, most obvious war, is the war between the humans of Zion and the machines. According to The Architect, this war is actually a planned part of the control mechanism. As it turns out, the real war is between The Oracle and the rest of the machines.
The Machines discover that she is working against them. Her program is considered rebellious, and she is given the option of being deleted or exiled. She chooses exile, knowing that she can still work from that position to achieve her goal of perfection within the Matrix.
The Neo-Smith connection is a second problem. Neo holds code that exposes the weaknesses of the Matrix. When he jumped into Smith at the end of the first movie, this code corrupted Smith’s program. Smith came back to “life” much stronger than before, and became a problem. Instead of temporarily taking over programs that are attached to human brains, he is now capable of permanently taking over machine programs as a means of replication. In the end, Smith becomes simply the motivation that allows the machines to cooperate with Neo. That’s all.
So, the bottom line for understanding the Matrix trilogy is this. The Oracle, using Neo, Morpheus, and the others from Zion as her army, is waging a war against the rest of the machines. The goal of this war is, quite simply, to remove problematic humans from the Matrix so that the rest can live in perfect harmony.
When you watch the movies again, pay close attention to the dialogue with The Oracle, The Architect, and Smith. All the clues are there, and understanding these clues are everything to making sense of The Matrix Trilogy.

Only thing is the humans in the film are part of the virus-the matrix is about the machine gaining its artificial intelligence. The ultimate self awareness…Episode 2 holds the key Neo and Zion are the sixth-maybe the seventh (I can’t remember) incarnation of the resistance…. The Oracle is the creator within the Matrix to promote self awareness and thus become human-like…she is part of the virus. There are no living humans they are part of the interdynamics of the matrix…RAP

Hi, I just want to say, Its really cool for the first time, I hear people understand the trilogy exactly the way I have. I just now and understood it fully this time, after it I just had to look if there were other people who really understood it as well..

Ok i totally agree with you-that is the basic of the matrix. But what makes this movies great is what lies beyond. This is something that kept me watching it over and over again for the past 14 years(note that when i first saw it I was 4). I still don’t get the whole of it and that’s the beauty of the movie. Every time I see it I find something new for me, whether it is something that I failed to notice or it’s something that I wasn’t ”grown” enough to understand. The matrix is a very complex movie this is what I like about it makes you think a lot.Just look up the symbolic meaning of every single name that appears in the matrix even the names of their ships-all of that has a reason to be there.